Microbes and Environments最新文献

{"title":"NH2OH Disproportionation Mediated by Anaerobic Ammonium-oxidizing (Anammox) Bacteria","authors":"M. Oshiki, Lin Gao, Lei Zhang, S. Okabe","doi":"10.1264/jsme2.ME21092","DOIUrl":"https://doi.org/10.1264/jsme2.ME21092","url":null,"abstract":"Anammox bacteria produce N2 gas by oxidizing NH4+ with NO2–, and hydroxylamine (NH2OH) is a potential intermediate of the anammox process. N2 gas production occurs when anammox bacteria are incubated with NH2OH only, indicating their capacity for NH2OH disproportionation with NH2OH serving as both the electron donor and acceptor. Limited information is currently available on NH2OH disproportionation by anammox bacteria; therefore, the stoichiometry of anammox bacterial NH2OH disproportionation was examined in the present study using 15N-tracing techniques. The anammox bacteria, Brocadia sinica, Jettenia caeni, and Scalindua sp. were incubated with the addition of 15NH2OH, and the production of 15N-labeled nitrogenous compounds was assessed. The anammox bacteria tested performed NH2OH disproportionation and produced 15-15N2 gas and NH4+ as reaction products. The addition of acetylene, an inhibitor of the anammox process, reduced the activity of NH2OH disproportionation, but not completely. The growth of B. sinica by NH2OH disproportionation (–240.3 kJ mol NH2OH–1 under standard conditions) was also tested in 3 up-flow column anammox reactors fed with 1) 0.7 mM NH2OH only, 2) 0.7 mM NH2OH and 0.5 mM NH4+, and 3) 0.7 mM NH2OH and 0.5 mM NO2–. NH2OH consumption activities were markedly reduced after 7 d of operation, indicating that B. sinica was unable to maintain its activity or biomass by NH2OH disproportionation.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41463425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"N2O Reduction by Gemmatimonas aurantiaca and Potential Involvement of Gemmatimonadetes Bacteria in N2O Reduction in Agricultural Soils","authors":"M. Oshiki, Yuka Toyama, T. Suenaga, A. Terada, Y. Kasahara, Takashi Yamaguchi, N. Araki","doi":"10.1264/jsme2.ME21090","DOIUrl":"https://doi.org/10.1264/jsme2.ME21090","url":null,"abstract":"Agricultural soil is the primary N2O sink limiting the emission of N2O gas into the atmosphere. Although Gemmatimonadetes bacteria are abundant in agricultural soils, limited information is currently available on N2O reduction by Gemmatimonadetes bacteria. Therefore, the effects of pH and temperature on N2O reduction activities and affinity constants for N2O reduction were examined by performing batch experiments using an isolate of Gemmatimonadetes bacteria, Gemmatimonas aurantiaca (NBRC100505T). G. aurantiaca reduced N2O at pH 5–9 and 4–50°C, with the highest activity being observed at pH 7 and 30°C. The affinity constant of G. aurantiaca cells for N2O was 4.4 μM. The abundance and diversity of the Gemmatimonadetes 16S rRNA gene and nosZ encoding nitrous oxide reductase in agricultural soil samples were also investigated by quantitative PCR (qPCR) and amplicon sequencing analyses. Four N2O-reducing agricultural soil samples were assessed, and the copy numbers of the Gemmatimonadetes 16S rRNA gene (clades G1 and G3), nosZ DNA, and nosZ mRNA were 8.62–9.65×108, 5.35–7.15×108, and 2.23–4.31×109 copies (g dry soil)–1, respectively. The abundance of the nosZ mRNA of Gemmatimonadetes bacteria and OTU91, OUT332, and OTU122 correlated with the N2O reduction rates of the soil samples tested, suggesting N2O reduction by Gemmatimonadetes bacteria. Gemmatimonadetes 16S rRNA gene reads affiliated with OTU4572 and OTU3759 were predominant among the soil samples examined, and these Gemmatimonadetes OTUs have been identified in various types of soil samples.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42373544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Population Distribution of Phosphate-solubilizing Microorganisms in Agricultural Soil","authors":"I. Djuuna, S. Prabawardani, Maria Massora","doi":"10.1264/jsme2.ME21041","DOIUrl":"https://doi.org/10.1264/jsme2.ME21041","url":null,"abstract":"Phosphorus (P) is an essential macronutrient for plant growth and is mainly present in agricultural soil in unavailable forms. Phosphate-solubilizing microorganisms (PSMs) increase soil P availability. The objective of the present study was to assess the population and type of PSMs and their relationships with soil characteristics in the agricultural soil of Manokwari. Twenty-one composite soil samples (0–20 cm) were collected at the rhizospheres of plants in the Prafi and Masni Districts. A dilution technique and plate count method on Pikovskayas agar medium were used to examine the PSM population, phosphate-solubilizing index (PSI), and various soil properties. The results obtained showed that the total population of phosphate-solubilizing bacteria ranged between 25×103 and 550×103 CFU g–1 of soil, while that of phosphate-solubilizing fungi was between 2.0×103 and 5.0×103 CFU g–1 of soil at all locations. The PSI of the isolates ranged between 1.1 to 3.6 mm, with the most efficient and highest PSI being obtained for Bacillus sp. (strain 8) and the lowest for Pseudomonas sp. (strain 15). Six isolates found at all locations were identified at the genus level: Chromobacterium sp., Pseudomonas sp., Bacillus sp., Micrococcus sp., Caulobacter sp., and Aspergillus sp. A correlation was observed between the number of PSMs and the level of soil P availability and moisture content, indicating an increase in soil P availability with a greater abundance of PSMs in soil.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42421486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Environmental Factors Affecting the Community of Methane-oxidizing Bacteria","authors":"Hiromi Kambara, Takahiro Shinno, Norihisa Matsuura, S. Matsushita, Y. Aoi, T. Kindaichi, N. Ozaki, A. Ohashi","doi":"10.1264/jsme2.ME21074","DOIUrl":"https://doi.org/10.1264/jsme2.ME21074","url":null,"abstract":"Methane-oxidizing bacteria (MOB) are ubiquitous and play an important role in the mitigation of global warming by reducing methane. MOB are commonly classified into Type I and Type II, belonging to Gammaproteobacteria and Alphaproteobacteria, respectively, and the diversity of MOB has been examined. However, limited information is currently available on favorable environments for the respective MOB. To investigate the environmental factors affecting the dominant type in the MOB community, we performed MOB enrichment using down-flow hanging sponge reactors under 38 different environmental conditions with a wide range of methane (0.01–80%) and ammonium concentrations (0.001–2,000 mg N L–1) and pH 4–7. Enrichment results revealed that pH was a crucial factor influencing the MOB type enriched. Type II was dominantly enriched at low pH (4–5), whereas Type I was dominant around neutral pH (6–7). However, there were some unusual cultivated biomass samples. Even though high methane oxidation activity was observed, very few or zero conventional MOB were detected using common FISH probes and primer sets for the 16S rRNA gene and pmoA gene amplification. Mycobacterium mostly dominated the microbial community in the biomass cultivated at very high NH4+ concentrations, strongly implying that it exhibits methane oxidation activity. Collectively, the present results revealed the presence of many unknown phylogenetic groups with the capacity for methane oxidation other than the reported MOB.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47224202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of New Halomonas Strains from Food-related Environments","authors":"Ayaka Tsuji, Y. Takei, Taku Nishimura, Y. Azuma","doi":"10.1264/jsme2.ME21052","DOIUrl":"https://doi.org/10.1264/jsme2.ME21052","url":null,"abstract":"Halomonas species, which are aerobic, alkaliphilic, and moderately halophilic bacteria, produce diverse biochemicals. To identify food-related Halomonas strains for bioremediation and the industrial production of biochemicals, 20 strains were isolated from edible seashells, shrimp, and umeboshi (pickled Japanese plum) factory effluents. All isolates were phylogenetically classified into a large clade of Halomonas species. Most isolates, which grew in wide pH (6–13) and salt concentration (0–14%) ranges, exhibited the intracellular accumulation of poly(3-hydroxybutyrate) granules. The characteristics of these isolates varied. A020 isolated from umeboshi factory effluents exhibited enhanced stress tolerance and proliferation and comprised two plasmids. IMZ03 and A020 grew to more than 200 OD600, while IMZ03 produced 3.5% 3-hydroxybutyrate in inorganic medium supplemented with 10% sucrose. The mucus of TK1-1 cultured on agar medium comprised approximately 64 mM of ectoine. Whole-genome sequencing of A020 was performed to elucidate its origin and genomic characteristics. The genome analysis revealed a region exhibiting synteny with a large virus genome isolated from the ocean, but did not identify any predictable pathogenic genes. Therefore, saline foods and related materials may be suitable resources for isolating Halomonas strains exhibiting unique, useful, and innocuous features.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47662541","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phenolic Acids Induce Nod Factor Production in Lotus japonicus–Mesorhizobium Symbiosis","authors":"M. Shimamura, Takashi Kumaki, Shun Hashimoto, K. Saeki, S. Ayabe, A. Higashitani, T. Akashi, Shusei Sato, T. Aoki","doi":"10.1264/jsme2.me21094","DOIUrl":"https://doi.org/10.1264/jsme2.me21094","url":null,"abstract":"In legume–rhizobia symbiosis, partner recognition and the initiation of symbiosis processes require the mutual exchange of chemical signals. Chemicals, generally (iso)flavonoids, in the root exudates of the host plant induce the expression of nod genes in rhizobia, and, thus, are called nod gene inducers. The expression of nod genes leads to the production of lipochitooligosaccharides (LCOs) called Nod factors. Natural nod gene inducer(s) in Lotus japonicus–Mesorhizobium symbiosis remain unknown. Therefore, we developed an LCO detection method based on ultra-high-performance liquid chromatography–tandem-quadrupole mass spectrometry (UPLC-TQMS) to identify these inducers and used it herein to screen 40 phenolic compounds and aldonic acids for their ability to induce LCOs in Mesorhizobium japonicum MAFF303099. We identified five phenolic acids with LCO-inducing activities, including p-coumaric, caffeic, and ferulic acids. The induced LCOs caused root hair deformation, and nodule numbers in L. japonicus inoculated with M. japonicum were increased by these phenolic acids. The three phenolic acids listed above induced the expression of the nodA, nodB, and ttsI genes in a strain harboring a multicopy plasmid encoding NodD1, but not that encoding NodD2. The presence of p-coumaric and ferulic acids in the root exudates of L. japonicus was confirmed by UPLC-TQMS, and the induction of ttsI::lacZ in the strain harboring the nodD1 plasmid was detected in the rhizosphere of L. japonicus. Based on these results, we propose that phenolic acids are a novel type of nod gene inducer in L. japonicus–Mesorhizobium symbiosis.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42833955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Endpoint Recombinase Polymerase Amplification (RPA) Assay for Enumeration of Thiocyanate-degrading Bacteria","authors":"M. Oshiki, T. Fukushima, Shuichi Kawano, Junichi Nakagawa","doi":"10.1264/jsme2.ME21073","DOIUrl":"https://doi.org/10.1264/jsme2.ME21073","url":null,"abstract":"An endpoint recombination amplification reaction (RPA) assay for assessing the abundance of the gene encoding thiocyanate dehydrogenase (TcDH) in Thiohalobacter has been developed. The RPA reaction was performed at 37°C for 30 min, terminated by the addition of sodium dodecyl sulfate (SDS) solution, and the DNA concentration of the RPA product was fluorometrically measured. The abundance of TcDH in 22 activated sludge samples and 7 thiocyanate-degrading enrichment cultures ranged between 2.5×103 and 1.5×106 copies μL–1, showing a linear relationship (R2=0.83) with those measured using a conventional quantitative PCR assay.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46187179","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Raman Micro-spectroscopy and Imaging of Filamentous Fungi.","authors":"Shinsuke Shigeto,&nbsp;Norio Takeshita","doi":"10.1264/jsme2.ME22006","DOIUrl":"https://doi.org/10.1264/jsme2.ME22006","url":null,"abstract":"<p><p>Filamentous fungi grow by the elongation of tubular cells called hyphae and form mycelia through repeated hyphal tip growth and branching. Since hyphal growth is closely related to the ability to secrete large amounts of enzymes or invade host cells, a more detailed understanding and the control of its growth are important in fungal biotechnology, ecology, and pathogenesis. Previous studies using fluorescence imaging revealed many of the molecular mechanisms involved in hyphal growth. Raman microspectroscopy and imaging methods are now attracting increasing attention as powerful alternatives due to their high chemical specificity and label-free, non-destructive properties. Spatially resolved information on the relative abundance, structure, and chemical state of multiple intracellular components may be simultaneously obtained. Although Raman studies on filamentous fungi are still limited, this review introduces recent findings from Raman studies on filamentous fungi and discusses their potential use in the future.</p>","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"37 6","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10037093/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9186581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High-resolution Microbiome Analyses of Nine Psyllid Species of the Family Triozidae Identified Previously Unrecognized but Major Bacterial Populations, including Liberibacter and Wolbachia of Supergroup O.","authors":"Atsushi Nakabachi,&nbsp;Hiromitsu Inoue,&nbsp;Yuu Hirose","doi":"10.1264/jsme2.ME22078","DOIUrl":"https://doi.org/10.1264/jsme2.ME22078","url":null,"abstract":"<p><p>Psyllids (Hemiptera: Sternorrhyncha: Psylloidea) are plant sap-sucking insects that include important agricultural pests. To obtain insights into the ecological and evolutionary behaviors of microbes, including plant pathogens, in Psylloidea, high-resolution ana-lyses of the microbiomes of nine psyllid species belonging to the family Triozidae were performed using high-throughput amplicon sequencing of the 16S rRNA gene. Analyses identified various bacterial populations, showing that all nine psyllids have at least one secondary symbiont, along with the primary symbiont \"Candidatus Carsonella ruddii\" (Gammaproteobacteria: Oceanospirillales: Halomonadaceae). The majority of the secondary symbionts were gammaproteobacteria, particularly those of the order Enterobacterales, which included Arsenophonus and Serratia symbiotica, a bacterium formerly recognized only as a secondary symbiont of aphids (Hemiptera: Sternorrhyncha: Aphidoidea). The non-Enterobacterales gammaproteobacteria identified in the present study were Diplorickettsia (Diplorickettsiales: Diplorickettsiaceae), a potential human pathogen, and Carnimonas (Oceanospirillales: Halomonadaceae), a lineage detected for the first time in Psylloidea. Regarding alphaproteobacteria, the potential plant pathogen \"Ca. Liberibacter europaeus\" (Rhizobiales: Rhizobiaceae) was detected for the first time in Epitrioza yasumatsui, which feeds on the Japanese silverberry Elaeagnus umbellata (Elaeagnaceae), an aggressive invasive plant in the United States and Europe. Besides the detection of Wolbachia (Rickettsiales: Anaplasmataceae) of supergroup B in three psyllid species, a lineage belonging to supergroup O was identified for the first time in Psylloidea. These results suggest the rampant transfer of bacterial symbionts among animals and plants, thereby providing deeper insights into the evolution of interkingdom interactions among multicellular organisms and bacteria, which will facilitate the control of pest psyllids.</p>","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"37 4","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9763047/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10466875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Novel Cross-domain Symbiosis between Candidatus Patescibacteria and Hydrogenotrophic Methanogenic Archaea Methanospirillum Discovered in a Methanogenic Ecosystem.","authors":"Kyohei Kuroda,&nbsp;Kengo Kubota,&nbsp;Shuka Kagemasa,&nbsp;Ryosuke Nakai,&nbsp;Yuga Hirakata,&nbsp;Kyosuke Yamamoto,&nbsp;Masaru K Nobu,&nbsp;Takashi Narihiro","doi":"10.1264/jsme2.ME22063","DOIUrl":"https://doi.org/10.1264/jsme2.ME22063","url":null,"abstract":"<p><p>To identify novel cross-domain symbiosis between Candidatus Patescibacteria and Archaea, we performed fluorescence in situ hybridization (FISH) on enrichment cultures derived from methanogenic bioreactor sludge with the newly designed 32-520-1066 probe targeting the family-level uncultured clade 32-520/UBA5633 lineage in the class Ca. Paceibacteria. All FISH-detectable 32-520/UBA5633 cells were attached to Methanospirillum, indicating high host specificity. Transmission electron microscopy observations revealed 32-520/UBA5633-like cells that were specifically adherent to the plug structure of Methanospirillum-like rod-shaped cells. The metagenome-assembled genomes of 32-520/UBA5633 encoded unique gene clusters comprising pilin signal peptides and type IV pilins. These results provide novel insights into unseen symbiosis between Ca. Patescibacteria and Archaea.</p>","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"37 4","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9763046/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10531137","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}